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annotate checkm2_plugin.xml @ 30:26ee5e11ecbe draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
author iuc
date Thu, 15 Jan 2026 20:39:44 +0000
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30
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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1 <macros>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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2 <token name="@CHECKM2_COMMAND@"><![CDATA[
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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3 #set $pattern = "Name\tCompleteness\tContamination\tCompleteness_Model_Used\tTranslation_Table_Used"
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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4 @LN_FILES@
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5 ]]></token>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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6 <xml name="checkm2_form">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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7 <param name="input" type="data" format="tabular" multiple="true" label="Output of CheckM2" help="It should be the quality report from CheckM2"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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8 </xml>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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9 <xml name="checkm2_test">
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iuc
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10 <test expect_num_outputs="3">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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11 <repeat name="results">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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12 <conditional name="software_cond">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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13 <param name="software" value="checkm2"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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14 <param name="input" value="checkm2.tsv"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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15 </conditional>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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16 </repeat>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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17 <param name="title" value="Title of the report"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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18 <param name="comment" value="Commment for the report"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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19 <param name="flat" value="true"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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20 <param name="export" value="true"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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21 <output name="html_report">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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22 <assert_contents>
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iuc
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23 <has_text text="Title of the report"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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24 <has_text text="Commment for the report"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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25 <has_text text="CheckM2"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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26 </assert_contents>
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iuc
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27 </output>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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28 <output_collection name="plots" type="list" count="0"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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29 </test>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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30 <!-- This test use a Checkm2 TSV file with wrong required headers to check error handling.
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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31 Some checkm2 column names are parameter-dependent and the checkm2 multiQC module rely on a specific column pattern.
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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32 An issue has been opened : https://github.com/MultiQC/MultiQC/issues/3466
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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33 There is a stdio rule in macro that need to be removed once the issue is fixed -->
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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34 <test expect_failure="true" expect_exit_code="1">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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35 <repeat name="results">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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36 <conditional name="software_cond">
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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37 <param name="software" value="checkm2"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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38 <param name="input" value="checkm2-wrong.tsv"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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39 </conditional>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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40 </repeat>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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41 <param name="title" value="Title of the report"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
iuc
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42 <param name="comment" value="Commment for the report"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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43 <param name="flat" value="true"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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44 <param name="export" value="true"/>
26ee5e11ecbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
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45 </test>
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46 </xml>
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47 </macros>